TABLE 2.
Primers designed for qRT-PCR
| Gene | Primer target | 5′–3′ sequencea | Product size (bp)b | Strain(s) amplified |
|---|---|---|---|---|
| Glyceraldehyde phosphate dehydrogenase | GAPDH | F: TGAAGGCGGTAACCTAATCG | 97 | All |
| R: TACGTCAACACCGATTGCAT | ||||
| Outer membrane lipoprotein | wza | F: TTGCCGGTTGTACTGTACCC | 79 | All |
| R: TCTTGGCTGCTATCGTTCAC | ||||
| Cognate phosphatase | wzb | F: GTAAGCCAGCCGATGCAATG | 98 | All |
| R: GCTACACAGCGCAGAGGTAA | ||||
| Tyrosine autokinase | wzc | F: GCTGCTTGGCATTCTTTTGGA | 93 | All |
| R: GTTGAAAGTAGCGCAACCGC | ||||
| Type IV pilin protein subunitc | pilA | F: TCATTGGTGTGTTAGCCGCA | 73 | JY1305 only |
| R: GCTGAGGCAGCTTCTGACTT | ||||
| Type IV pilin protein subunitc | pilA | F: TTGCTAAAAGTGAAGCCGCA | 169 | JY1701 only |
| R: CCAGCTGCACTAGTAGGGTT | ||||
| Type IV pilin protein subunitc | pilA | F: GCACAGCTCCAACCAGTAGT | 57 | CMCP6, MO6-24 |
| R: TTGGCGGCACTTCAACAATG | ||||
| Type IV pilin protein prepilinc peptidase | pilD | F: GGCTTACTGGTAGGCAGCTT | 126 | JY1701, JY1305 |
| R: GGTTTCTGTCGGCGGTGATA | ||||
| Type IV pilin protein prepilinc peptidase | pilD | F: TTGGCTTACTGGTAGGCAGC | 128 | CMCP6, MO6-24 |
| R: GGTTTCTGTCGGTGGTGTGA | ||||
| Mannitol-sensitive hemagglutinin | mshA | F: CAAGGCGGTTTCACCCTGAT | 90 | All |
| R: CAGATTTAGAAAACGCGGAGCC | ||||
| Flagellar monomeric hook subunit | flgE | F: TCTAACTGAGCTGCGGACAA | 145 | All |
| R: TACTGCTCAATCTGGCTGGC |
a
F, forward primer target; R, reverse primer target.
b
Products amplified between sequenced strains in silico.
c
Primers designed for this gene were different between strains/genotypes.